Multiplexing assays are another speed-booster. GenArraytion’s microsequencing method, Sniper Sequencing, allows researchers to perform multiple analyses in parallel that generally are performed sequentially, according to R. Paul Schaudies, Ph.D., CEO.
Sniper Sequencing provides a functionally complete characterization of a broad spectrum of microorganisms within hours, he said. It combines information about the functional elements of pathogens with information about their specific signatures to provide a detailed fingerprint that accurately characterizes organisms to strain and isolate levels on platforms such as the CombiMatrix microarray. That capability allows scientists to genetically characterize unknown strains and to determine whether those strains have been genetically manipulated.
The company has an SBIR grant to develop the technology for characterizing strains of drug-resistant Staphylococcus aureus (MRSA) bacteria. That project uses genetic sequences from a wide range of staph strains to generate detailed hybridization profiles for organisms with no published sequences.
In the second phase of the project, “GenArraytion has an agreement with two major medical centers to provide clinical isolates with antibiotic growth profiles for genomic characterization using Sniper Sequencing. GenArraytion plans to select a subset of 4,400 oligonucleotides that correlate with antibody susceptibility profiles to provide rapid, accurate treatment,” said Dr. Schaudies.
Working with the Luminex beaded array platform, GenArraytion will use functional and unique genetic sequences to provide a more relevant signature subset that will be transferred to smaller, faster beaded arrays for point-of-care diagnostics, he explained. The goal is to provide an assay to identify and determine the antibiotic susceptibility of MRSA viruses for the hospital critical-care market to identify hospital-acquired and community-acquired MRSA strains and to determine antibiotic susceptibility.
Speed is one of this system’s key benefits. Normally, in treating septic infections, traditional microbiological methods for identifying pathogens and determining their sensitivity to particular antibiotics requires four or more days. GenArraytion’s approach will require less than six hours, added Dr. Schaudies. Therefore, physicians can treat immediately with an effective antibiotic rather than using a broad-spectrum cocktail while awaiting test results. That difference speeds patients’ recoveries and extends the useful life of existing antibiotics.
Sniper Sequencing technology can be applied to veterinary diagnostics, biological defense, epidemiological monitoring, environmental testing, and food and water safety. GenArraytion has worked with several U.S. government agencies to develop detailed signatures for organisms that pose a threat to human and animal health, including an effort with the U.S. EPA to identify multiple oligonucleotide differences among strains of Cryptosporidium parvum and hominis.
Atlas Genetics has developed a portable, integrated cartridge and instrument system that combines sample preparation, DNA amplification, and detection to deliver results within 25 minutes. “The first test is for chlamydia; it will be in clinical trials in 2011,” according to John Clarkson, Ph.D., CEO. “The first clinical trials showed a sensitivity of 96% and specificity of 98% against the gold standard. Limit of detection for chlamydia is approximately 10 cells.”
The system runs on the Velox platform, which detects DNA and RNA from clinical samples using electrochemistry. Optical clarity is not an issue. It is designed initially for clinical diagnostics but can be used for other analytes, multiplexing up to 20 analytes per cartridge. Because this is designed as a CLIA-waived system, it can be used at point of care.
“The next test will be chlamydia and gonorrhea combined, and we are also developing a test in collaboration with the U.K.’s Animal Health Trust for equine strangles, which is caused by Streptococcus equi,” Dr. Clarkson said. Other tests are in development for MRSA, group B streptococcus, and Norwalk viruses in humans.